Cut beef chuck in half; cut each half into 3–4-inch pieces. Cut each beef short rib through the middle, all the way down to the bone.
In a dry skillet over medium heat, toast guajillo and ancho chiles for 30 seconds per side until fragrant (avoid burning).
Place toasted chiles in a bowl and cover with hot water; let soak 15 minutes until softened.
Drain chiles and transfer to a blender. Add onion, garlic cloves, cumin, oregano, cinnamon, cloves, and 1 cup of beef broth. Blend until smooth.
Season beef pieces generously with salt and pepper, then coat evenly with the chile-spice puree.
Heat vegetable oil in a large Dutch oven over medium-high heat. Sear the beef and ribs in batches until browned on all sides, about 3–4 minutes per side.
Pour remaining beef broth into the pot, add bay leaves, and bring to a gentle simmer.
Cover and transfer to a 250°F oven or lower stovetop heat. Cook for 4–6 hours, or until meat is fork-tender and falling off the bone.
Remove meat and bones; shred beef with two forks, discarding bones. Skim excess fat from the surface of the broth.
Return shredded beef to the pot, stir, and serve hot. Garnish with cilantro, diced onion, and lime wedges for tacos or serve as a hearty stew.